Rendering rmarkdown files #32
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| name: render-rmarkdown | |
| run-name: Rendering rmarkdown files | |
| on: [push] | |
| jobs: | |
| render-rmarkdown: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Install libraries | |
| run: | | |
| sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev | |
| sudo apt-get install libharfbuzz-dev libfribidi-dev libfreetype6-dev libfontconfig1-dev | |
| - name: Install dependencies | |
| run: | | |
| install.packages("textshaping") | |
| install.packages("curl") | |
| install.packages("devtools") | |
| install.packages("BiocManager") | |
| install.packages("rmarkdown") | |
| devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories()) | |
| devtools::install_github("satijalab/seurat", "seurat5") | |
| install.packages("Signac") | |
| BiocManager::install("destiny") | |
| shell: Rscript {0} | |
| - name: Install packages for tutorial | |
| run: | | |
| devtools::install_github("immunogenomics/harmony") | |
| BiocManager::install("Nebulosa") | |
| BiocManager::install("JASPAR2020") | |
| BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") | |
| BiocManager::install("EnsDb.Hsapiens.v86") | |
| devtools::install_github("CostaLab/MOJITOO") | |
| install.packages('ggraph') | |
| install.packages('igraph') | |
| shell: Rscript {0} | |
| - name: Install scMEGA | |
| run: | | |
| devtools::install_github("CostaLab/scMEGA") | |
| shell: Rscript {0} | |
| # - name: Render Rmarkdown files | |
| # run: | | |
| # pkgdown::build_site() | |
| # shell: Rscript {0} | |
| - name: Render Rmarkdown files | |
| run : | | |
| pkgdown::build_article(name='install.Rmd', quiet=FALSE) | |
| shell: Rscript {0} | |
| - name: Commit files | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| git commit -am "Re-build Rmarkdown files" | |
| git push origin || echo "No changes to commit" |